Current challenges for de novo Hevea brasiliensis genome sequencing

The fRRDB Biotechnology Group recommended in 2009 the generation of a reference sequence of rubber genome in order to ease resequencing of genome for commercial clones, to accelerate breeding programmes, and to improve functional understanding of plants and consequent rubber production. So far, several national initiatives have been launched in China, Malaysia and United Kingdom, and likely in Japan and Thailand. Although genome sequence of major crops is available, only a draft sequence was published for rubber. This paper presents an overview of these different initiatives. De novo sequencing was carried out on clones Reyan7-33-97, RRlM 600, and RRfM 928. These genomes were assembled in a large number of scaffolds (7,700; 608,017 and 954,373 scaffolds, respectively) far from the 18 chromosomes of the haploid rubber genome. Rubber clones are highly heterozygous and have a high frequency of repeat sequences. These constraints are supposed to hamper the delivery of a full sequence of rubber genome. New strategies for de novo sequencing and interactions between these different initiatives were suggested to overcome these issues. (Résumé d'auteur